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基本情報
登録情報 | データベース: PDB / ID: 8d4d | ||||||||||||
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タイトル | gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes | ||||||||||||
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![]() | PROTEIN TRANSPORT / nef / AP / trafficking | ||||||||||||
機能・相同性 | ![]() basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization ...basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / Glycosphingolipid transport / regulation of receptor internalization / melanosome assembly / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / Golgi to vacuole transport / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / Synthesis of PIPs at the Golgi membrane / Golgi Associated Vesicle Biogenesis / symbiont-mediated suppression of host apoptosis / clathrin adaptor activity / suppression by virus of host autophagy / MHC class II antigen presentation / CD4 receptor binding / Nef Mediated CD4 Down-regulation / thioesterase binding / dendritic spine organization / determination of left/right symmetry / long-term synaptic depression / clathrin-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Lysosome Vesicle Biogenesis / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / clathrin binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / Golgi Associated Vesicle Biogenesis / CD8 receptor binding / cell leading edge / antigen processing and presentation of exogenous peptide antigen via MHC class I / MHC class I protein binding / endoplasmic reticulum exit site / host cell Golgi membrane / Synthesis of PIPs at the plasma membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / intracellular copper ion homeostasis / protein targeting / beta-2-microglobulin binding / COPI-mediated anterograde transport / T cell receptor binding / detection of bacterium / clathrin-coated pit / regulation of calcium-mediated signaling / vesicle-mediated transport / viral life cycle / MHC class II antigen presentation / Neutrophil degranulation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / small monomeric GTPase / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / kidney development / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / MHC class I peptide loading complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / cellular response to virus / MHC class I protein complex / SH3 domain binding / virion component / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of type II interferon production / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / Interferon alpha/beta signaling / E3 ubiquitin ligases ubiquitinate target proteins / early endosome membrane / ATPase binding / presynapse 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
手法 | 電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 9.6 Å | ||||||||||||
![]() | Hooy, R.M. / Hurley, J.H. | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat. 著者: Richard M Hooy / Yuichiro Iwamoto / Dan A Tudorica / Xuefeng Ren / James H Hurley / ![]() 要旨: The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to ...The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to sequester major histocompatibility complex class I (MHC-I), evading immune detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated membranes without clathrin and determined its structure. The coat assembles via Arf1 dimer interfaces. AP-1-positive tubules are enriched in cells upon clathrin knockdown. Nef localizes preferentially to AP-1 tubules in cells, explaining how Nef sequesters MHC-I. Coat contact residues are conserved across Arf isoforms and the Arf-dependent AP complexes AP-1, AP-3, and AP-4. Thus, AP complexes can self-assemble with Arf1 into tubular coats without clathrin or other scaffolding factors. The AP-1:Arf1 coat defines the structural basis of a broader class of tubulovesicular membrane coats as an intermediate in clathrin vesicle formation from internal membranes and as an MHC-I sequestration mechanism in HIV-1 infection. | ||||||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 675.4 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 27182MC ![]() 7ux3C ![]() 8d4cC ![]() 8d4eC ![]() 8d4fC ![]() 8d4gC ![]() 8d9rC ![]() 8d9sC ![]() 8d9tC ![]() 8d9uC ![]() 8d9vC ![]() 8d9wC C: 同じ文献を引用 ( M: このデータのモデリングに利用したマップデータ |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
-タンパク質 , 2種, 8分子 CHDFNLKI
#1: タンパク質 | 分子量: 20590.547 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: N-terminal myristoylation / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 24154.049 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: N-terminal myristoylation 由来: (組換発現) ![]() ![]() 遺伝子: nef / 発現宿主: ![]() ![]() |
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-タンパク質・ペプチド , 1種, 2分子 YP
#3: タンパク質・ペプチド | 分子量: 4139.429 Da / 分子数: 2 / Mutation: T345S, S349G, G355S, C363A / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-AP-1 complex subunit ... , 4種, 8分子 BAGEMJSO
#4: タンパク質 | 分子量: 104736.461 Da / 分子数: 2 / Mutation: K359R, E476K / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #5: タンパク質 | 分子量: 68194.094 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #6: タンパク質 | 分子量: 48606.730 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #7: タンパク質 | 分子量: 18305.273 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-非ポリマー , 2種, 8分子 ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#8: 化合物 | ChemComp-GTP / #9: 化合物 | ChemComp-MG / |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: サブトモグラム平均法 |
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試料調製
構成要素 |
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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.2 詳細: HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments. | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||||||||||||
試料支持 | グリッドのタイプ: EMS Lacey Carbon | |||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 298 K 詳細: 60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted. |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 42000 X / 最大 デフォーカス(公称値): 4500 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 2.7 mm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 3 sec. / 電子線照射量: 3 e/Å2 / Avg electron dose per subtomogram: 123 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 詳細: Tilt images were collected in movie-mode. Each movie/tilt consisted of 3-4 frames each |
電子光学装置 | エネルギーフィルタースリット幅: 25 eV |
画像スキャン | 横: 5760 / 縦: 4092 |
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解析
ソフトウェア |
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EMソフトウェア |
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画像処理 | 詳細: The images were gain-normalized | ||||||||||||||||||||||||||||||||
CTF補正 | 詳細: CTF was estimated on a per-tilt basis in IMOD (4.11) using CTFPLOTTER. The results were used as input to NOVACTF during 3DCTF correction. タイプ: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 9.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 7343 / アルゴリズム: BACK PROJECTION / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
EM volume selection | 詳細: Tubes were annotated by tracing the center of the tube in Dynamo and recording the average apparent diameter. Initial subtomogram positions were picked using uniform radial and axial sampling. Num. of tomograms: 38 / Num. of volumes extracted: 29941 / Reference model: Reference-free | ||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT | ||||||||||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model
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精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 32.79 Å2 | ||||||||||||||||||||||||||||||||
拘束条件 |
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